Structural biology in the clouds: the WeNMR-EOSC ecosystem

RV Honorato, PI Koukos, B Jiménez-García… - Frontiers in molecular …, 2021 - frontiersin.org
Structural biology aims at characterizing the structural and dynamic properties of biological
macromolecules at atomic details. Gaining insight into three dimensional structures of …

DeepRank: a deep learning framework for data mining 3D protein-protein interfaces

N Renaud, C Geng, S Georgievska… - Nature …, 2021 - nature.com
Abstract Three-dimensional (3D) structures of protein complexes provide fundamental
information to decipher biological processes at the molecular scale. The vast amount of …

Modeling and structure determination of homo-oligomeric proteins: An overview of challenges and current approaches

A Gaber, M Pavšič - International journal of molecular sciences, 2021 - mdpi.com
Protein homo-oligomerization is a very common phenomenon, and approximately half of
proteins form homo-oligomeric assemblies composed of identical subunits. The vast majority …

Biological vs. crystallographic protein interfaces: An overview of computational approaches for their classification

K Elez, AMJJ Bonvin, A Vangone - Crystals, 2020 - mdpi.com
Complexes between proteins are at the basis of almost every process in cells. Their study,
from a structural perspective, has a pivotal role in understanding biological functions and …

Biocatalytically active and stable cross‐linked enzyme crystals of halohydrin dehalogenase HheG by protein engineering

M Staar, S Henke, W Blankenfeldt… - ChemCatChem, 2022 - Wiley Online Library
A major drawback for practical application of halohydrin dehalogenase HheG in biocatalysis
is its rather low thermal stability and low organic solvent tolerance. We therefore pursued a …

Computational analysis of the functional and structural impact of the most deleterious missense mutations in the human Protein C

M Farajzadeh-Dehkordi, L Mafakher, A Harifi… - Plos one, 2023 - journals.plos.org
Protein C (PC) is a vitamin K-dependent factor that plays a crucial role in controlling
anticoagulant processes and acts as a cytoprotective agent to promote cell survival. Several …

Structure and dynamic association of an assembly platform subcomplex of the bacterial type II secretion system

R Dazzoni, Y Li, A López-Castilla, S Brier, A Mechaly… - Structure, 2023 - cell.com
Type II secretion systems (T2SSs) allow diderm bacteria to secrete hydrolytic enzymes,
adhesins, or toxins important for growth and virulence. To promote secretion of folded …

PINDER: The protein interaction dataset and evaluation resource

D Kovtun, M Akdel, A Goncearenco, G Zhou, G Holt… - bioRxiv, 2024 - biorxiv.org
Protein-protein interactions (PPIs) are fundamental to understanding biological processes
and play a key role in therapeutic advancements. As deep-learning docking methods for …

Staphylococcus aureus Exfoliative Toxin E, Oligomeric State and Flip of P186: Implications for Its Action Mechanism

C Gismene, JE Hernandez Gonzalez… - International Journal of …, 2022 - mdpi.com
Staphylococcal exfoliative toxins (ETs) are glutamyl endopeptidases that specifically cleave
the Glu381-Gly382 bond in the ectodomains of desmoglein 1 (Dsg1) via complex action …

QSalignWeb: A server to predict and analyze protein quaternary structure

S Dey, J Prilusky, ED Levy - Frontiers in molecular biosciences, 2022 - frontiersin.org
The identification of physiologically relevant quaternary structures (QSs) in crystal lattices is
challenging. To predict the physiological relevance of a particular QS, QSalign searches for …